Buggy code:
transcriptVariation . add ( tv ) ; } } List < String > resultVariationSynonym = queryByVariationId ( variationId , "variation_synonym" , variationDirectoryPath ) ; xrefs = new ArrayList ( ) ; if ( ( resultVariationSynonym != null ) && ( ( resultVariationSynonym . size ( ) ) > 0 ) ) { String [ ] arr ; for ( String rxref : resultVariationSynonym ) { variationSynonymFields = rxref . split ( "\t" ) ; if ( ( sourceMap . get ( variationSynonymFields [ 3 ] ) ) != null ) { arr = sourceMap . get ( variationSynonymFields [ 3 ] ) . split ( "," ) ; xrefs . add ( new Xref ( variationSynonymFields [ 4 ] , arr [ 0 ] , arr [ 1 ] ) ) ; } } } try { if ( ( variationFeatureFields != null ) && ( ( variationFeatureFields [ 6 ] ) != null ) ) { allelesArray = variationFeatureFields [ 6 ] . split ( "//" ) ; if ( ( allelesArray . length ) == 1 ) { allelesArray = new String [ ] { "" , "" } ; } } else { allelesArray = new String [ ] { "" , "" } ; } chromosome = seqRegionMap . get ( variationFeatureFields [ 1 ] ) ; consequenceTypes = ( variationFeatureFields != null ) ? Arrays . asList ( variationFeatureFields [ 12 ] . split ( "," ) ) : Arrays . asList ( "intergenic_variant" ) ; <START_BUG> if ( ( consequenceTypes . size ( ) ) == 0 ) { <END_BUG> displayConsequenceType = consequenceTypes . get ( 0 ) ; } else { for ( String cons : consequenceTypes ) { if ( ! ( cons . equals ( "intergenic_variant" ) ) ) { displayConsequenceType = cons ; break ; } } } variation = new Variation ( ( ( ( variationFields [ 2 ] ) != null ) && ( ! ( variationFields [ 2 ] . equals ( "\\N" ) ) ) ? variationFields [ 2 ] : "" ) , chromosome , "SNV" , ( variationFeatureFields != null ? Integer . parseInt ( variationFeatureFields [ 2 ] ) : 0 ) , ( variationFeatureFields != null ? Integer . parseInt ( variationFeatureFields [ 3 ] ) : 0 ) , variationFeatureFields [ 4 ] , ( ( ( allelesArray [ 0 ] ) != null ) && ( ! ( allelesArray [ 0 ] . equals ( "\\N" ) ) ) ? allelesArray [ 0 ] : "" ) , ( ( ( allelesArray [ 1 ] ) != null ) && ( ! ( allelesArray [ 1 ] . equals ( "\\N" ) ) ) ? allelesArray [ 1 ] : "" ) , variationFeatureFields [ 6 ] , ( ( ( variationFields [ 4 ] ) != null ) && ( ! ( variationFields [ 4 ] . equals ( "\\N" ) ) ) ? variationFields [ 4 ] : "" ) , displayConsequenceType , consequenceTypes , transcriptVariation , null , null , null , xrefs , ( ( ( variationFeatureFields [ 16 ] ) != null ) && ( ! ( variationFeatureFields [ 16 ] . equals ( "\\N" ) ) ) ? variationFeatureFields [ 16 ] : "" ) , ( ( ( variationFeatureFields [ 17 ] ) != null ) && ( ! ( variationFeatureFields [ 17 ] . equals ( "\\N" ) ) ) ? variationFeatureFields [ 17 ] : "" ) , ( ( ( variationFeatureFields [ 11 ] ) != null ) && ( ! ( variationFeatureFields [ 11 ] . equals ( "\\N" ) ) ) ? variationFeatureFields [ 11 ] : "" ) , ( ( ( variationFeatureFields [ 20 ] ) != null ) && ( ! ( variationFeatureFields [ 20 ] . equals ( "\\N" ) ) ) ? variationFeatureFields [ 20 ] : "" ) ) ; if ( ( ( ( ++ countprocess ) % 10000 ) == 0 ) && ( countprocess != 0 ) ) { logger . debug ( ( "Processed<seq2seq4repair_space>variations:<seq2seq4repair_space>" + countprocess ) ) ; } serializer . serialize ( variation ) ;

Fix:
if ( ( consequenceTypes . size ( ) ) == 1 ) {